Gilroy’s latest project, “The Bourne Legacy,” has had a complicated journey to the screen. Damon’s character was popular but had already solved the central problem of the trilogy, which was finding his true identity. A fourth movie entered the murky territory of Internet rumors until Damon and the director Paul Greengrass disengaged themselves from the project. (Damon had some rather harsh words for Gilroy’s work that he shared in a “GQ” cover story that he later apologized for, and Gilroy is more or less mum on the matter.)

Other people were interested in making a fourth, though, especially folks at Universal. Gilroy was brought in to chat about a new script, and once his gears started turning on what would become “Legacy,” he was hot to direct it.

One warm Friday morning, I sought out a mysterious steel door in a high-rise in Manhattan to meet with Gilroy himself and chat about the latest “Legacy,” post-9/11 politics, his multifaceted female characters and much more.

As you were developing this script, what about it made you passionate enough to say, “I want to direct it. Let me get my hands on it.”
The character. Everything else before that was kind of fun and games. I came in very incrementally… It wasn’t something I was really looking for… I thought, oh, here’s a cool idea for how to do it and some really cool writer-sexy structural things, but I thought [that] we’re never gonna find a character that has the sort of fundamental roots that Jason Bourne had… You know, the kind of issues and the kind of depth to his problem [that] sustained three pictures. It really was a pretty tough thing to meet. And when the character [Aaron Cross] came into view and his problem and his history, that’s when it got really interesting to me and that’s when the whole story sort of just fell into place… It’s going to be two years of your life and you’re looking to have something — is there enough here to nourish you for two years? So that’s when I got interested.

Specifically the aspect of his cognitive and physical boosts, is that what interests you? The scientific background?
Well, his history more than anything else. The boosts that he’s getting, these sort of enhancements that we’re talking about, they’re very, very minor things. They’re very small, and I think the reality is, there’s very little science fiction — there’s no science fiction in this at all. I think in ten, fifteen years, people will look back on this [and] the science will look very crude. This will be something that will be much more discussed and much more part of the conversation, but it was what he was risking [that] was way more interesting to me. The fact that he had really — where he comes from and, I don’t want to give away everything about it, but the shadow life that he lived before and his origins [were what] really spoke to me.

There’s a very key scene in the movie where this, exactly what we’re talking about, was really raising a question, where Rachel Weisz says to him, “Why is it so important to you?” And when he tells her why it’s so important to him — I mean, that’s where I started. And that concept, in a way, was way more personal to me than anything that I’d ever written about in Jason Bourne. I never was an assassin. I never had those kind of moral questions. Those are all imaginings. But the problem that Jeremy Renner’s character is facing in this film, if he fails, is something I think everybody thinks about at some time and certainly I do, [which is] what would it be like to have a diminishment in who you are? What if I sort of turned the power down in your head in a pretty significant way? It was more what he was risking than what he was gaining, that was the thing that was most interesting to me.

Yeah, it had a sort of “Flowers For Algernon” feel.
Very much.

You look at science today and you see people experimenting with nootropic drugs that make you faster and smarter, so it seems to be definitely something of interest. Similarly, the way all the Bourne movies have reflected society, technology, politics — how do you see these as a whole? How have they evolved politically along with the changes that we’ve seen? I see Jason Bourne very much as a 9/11 kind of character.
Very much.

All of the characters talk about patriotism. They’re doing this in the name of America, but they’re kind of like the sin eater [Norton mentions]. I’m curious as to your take on the evolution of that.
It’s not what you plan on, it’s sort of the residue of, I guess, how I feel and how the people making the films have felt along the way. We started pre-9/11. “Identity” is a really interesting story in that sense. It started pre-9/11 and then it wasn’t finished and there was a lot of extra work to do. 9/11 happens, the movie’s pushed back, it goes through a lot of very interesting changes as we’re trying to fix the movie, and it actually sort of spasms back to almost — there was a sort of a knee-jerk post-9/11 reaction. We actually worked on some scenes and some endings for that, and then enough time had passed and we came back to something that we’d had before.

We’re not in the villain business. We don’t have the guy who’s gonna take all the diamonds and put them on the moon and crash it into the Earth. We don’t have villains; the villains are all the people themselves. Jason Bourne’s biggest enemy is his own history. So there was a big morality play in those three films, and I think America’s gone through a big morality play in the last ten, eleven years. As we’re pulling back the curtain this time, as we’re going much, much wider and we’re seeing that Edward Norton’s been the mastermind of all this — if you’re gonna have the mastermind, you really need to know what his world view is and what his moral philosophy is that’s driving all this. And he has a very developed, very articulated, eyes-wide-open conscious view… There are terrible things that need to be done to keep us safe, and this is how I feel. There are terrible things being done on my behalf to keep me safe. I’m very conflicted about it. I want to be safe. I don’t like many of the things that are probably done with my tax dollar to do that. That tension is really interesting. He’s made a real conscious decision about where he falls on that and that someone has to do it. It’s time, in this picture, to have that idea presented.

Rachel Weisz’s character is carrying a different kind of moral dilemma. She’s a scientist working [on] one of these programs who’s so excited by the work she’s doing and so well-compensated for it and so confirmed by it that she’s, as bright as she is, she’s managed to build a very successful denial and naïveté about the actual practical application of her work.

I’m very interested in all of the female characters you’ve written — Rachel Weisz, of course Tilda Swinton’s character in “Michael Clayton,” all of them, especially in terms of the fact that Rachel Weisz is, give or take a year, actually Jeremy Renner’s age, which is not something you see in Hollywood. Do you ever get push back from studios, like, “We need someone younger.” Rachel Weisz is gorgeous and amazing, but do you ever have someone that’s like, “We need a sexy young thing to run with a gun”?
There are probably people who would have been happy with that. But I think that, as difficult and complicated as a lot of things have been to put together in every way, the one thing that makes this really simple when you work on this is every single decision you’re making as a writer, as a director, everything, every decision, it doesn’t matter if it’s casting or the set or the wardrobe or whatever, everything we do, we navigate towards authenticity. We’re trying all the time to be authentic and real, whether it’s behavior or… It would be so inappropriate to take some hottie and put glasses on her and say she’s a double doctorate…. It’s an easy argument to make when someone says, “We need X to play the part because it’s just that much cooler.” It’s a really easy argument to make. It’s a really clear thing to go towards all the time.

Right, but you push back against that.
I push back against, yes. A lot of pushing. All the time.

I think it speaks to you as a writer and a director the kind of complex female characters we see.
Well, they’re characters, you know? The whole thing about writing for women or writing for men, I’ve never [understood it]. You gotta believe in every single one of them. Every time you’re in somebody, every time you’re writing their point of view, you gotta believe in all of them… I don’t know, I’ve never been an assassin either. I’ve never been a doctor… And I know a lot more women than I know assassins. You try to write every character and believe in every single one of them.

There’s a scene where Aaron fights a wolf. “The Grey” and Joe Carnahan got some flack for their portrayals of wolves and so forth in the movie. It’s a difficult scene to watch, and I was wondering if you used creature effects, and if you’re curious if people will take issue with it?
It’s a chapter in our film, number one. Number two, there’s an explanation for… an enigmatic, sort of mysterious [explanation] but it is mentioned why the wolves are interested in him. And it’s a mythic part of the movie, in a way. There’s something sort of hopefully a little bit mythic about it. I never saw “The Grey” because I was very conscious of not wanting to see it since we were involved in making our own sequence. How we did it is really everything, every technique that’s available. There’s real wolves, there’s all kinds of ways of doing other things, movie magic. It takes everything that’s available — mechanically, visual effects wise and real wolves — to make it work. It was a long process to get it right.

Without giving it away, the one specific wolf is obviously CGI or creature…
A lot of it is a real wolf… You also have to understand that when you’re doing things, a lot of the modeling and stuff has to be done with real animals as well. So it’s really complicated. I hate movie magic being exposed, particularly before people see movies. Afterwards, I don’t mind, but because everything we do is so photo real, because what we’re presenting has to be so photo real, how we do it is less important to me to explain now, but it’s everything in the bag. It’s a lot of different techniques.

How many times have you seen asked about the Matt Damon thing?
Which Matt Damon thing?

His statements in GQ about the last Bourne movie.
Is that your question? How many times I’ve been asked about it? [joking] Six.

How tired are you of…
No, it doesn’t come up that often.

Really?
No.

Because there’s an obvious opportunity for him to come back. Do you think that’s feasible?
Frank Marshall, like a month ago said, “Oh, it would be my dream to see…” [And] two days later, it’s like, it’s happening. No one has ever talked about it. There’s no — there is absolutely no — you won’t believe me and no one ever [does] — there is no master plan. No one has discussed what’s going to happen next. I think that we’re going to come out next Friday and the audience is going to have a tremendous amount to say about what happens next, and all kinds of possibilities are open, but there is no — there’s not even any kind of specific discussion [that] has ever even happened, so I don’t know anything about it. I really don’t.

But interpersonally, would it be a problem?
Interpersonally would it be a problem?

Yeah.
Oh, I don’t even know. I don’t know how to answer that. I don’t really know. I haven’t spoken to [Damon] in years. I don’t really know.